BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 012308
(466 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JUR|A Chain A, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|B Chain B, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|C Chain C, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|D Chain D, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
Length = 448
Score = 165 bits (418), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 126/406 (31%), Positives = 188/406 (46%), Gaps = 55/406 (13%)
Query: 41 HSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTGSFDLISHLTL 100
V++ +FGA GDG T +++F+ AI + +GG +L VP G +LTG L S++ L
Sbjct: 26 REVNLLDFGARGDGRTDCSESFKRAI---EELSKQGGGRLIVPEGVFLTGPIHLKSNIEL 82
Query: 101 WLDKDAVILGSTNSDTWPVIDPLPSYGRGRELPGGRHRSLIFGRNLTDVVITGDNGTIDG 160
+ K + PV+ L + G EL + L++ + +V ITG +G +DG
Sbjct: 83 HV-KGTIKFIPDPERYLPVV--LTRF-EGIELYN--YSPLVYALDCENVAITG-SGVLDG 135
Query: 161 QG--SIWWEWFRN----------------------------------GTLDYTRPHLVEL 184
WW W G Y RP V+
Sbjct: 136 SADNEHWWPWKGKKDFGWKEGLPNQQEDVKKLKEMAERGTPVEERVFGKGHYLRPSFVQF 195
Query: 185 MNSTGVIISNLTFLNPPFWTIHPVYCSHVKVQNVTIRAPLDSPNTDGIDPDSSDDVCIKD 244
V++ + +N P W IHPV +V ++N+ I + PN DGIDP+S + I+
Sbjct: 196 YRCRNVLVEGVKIINSPMWCIHPVLSENVIIRNIEISST--GPNNDGIDPESCKYMLIEK 253
Query: 245 CYISTGDDLVSIKSGWDEYGISYGRPSTKITIH-GLIGETKLGAGIAIGSEMSGGVSEVH 303
C TGDD V IKSG D G G PS I + L+ G+ IGSEMSGGV V
Sbjct: 254 CRFDTGDDSVVIKSGRDADGRRIGVPSEYILVRDNLVISQASHGGLVIGSEMSGGVRNVV 313
Query: 304 AENLYFFNSVRGIRIKTSPGRGGYVRNI-SISNVTLNHVDVAIIFTGHFGEHPDDSYDPS 362
A N + N R +R+KT+ RGGY+ NI I NV +N + I + D+ +
Sbjct: 314 ARNNVYMNVERALRLKTNSRRGGYMENIFFIDNVAVNVSEEVIRINLRY-----DNEEGE 368
Query: 363 ALPIIERITIKNVIGENVKMAGQLEGIEGDTFRYICLSNIKLNGVS 408
LP++ + +KN+ K A ++EG+E D + I +S+ + G
Sbjct: 369 YLPVVRSVFVKNLKATGGKYAVRIEGLENDYVKDILISDTIIEGAK 414
>pdb|2UVE|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVE|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVF|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
pdb|2UVF|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
Length = 608
Score = 104 bits (260), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 114/464 (24%), Positives = 196/464 (42%), Gaps = 92/464 (19%)
Query: 11 FLVLALFSEAPWAVAGSSQCSQSNLEVFRPHSVSITEFGAVGDGVTLNTKAFQNAIFYLN 70
F V A +++ +VA ++++ +P V++ +FGA+ DG TLNTKA Q AI
Sbjct: 128 FTVKAQYADGSLSVASKPITAKTSA---KPQIVNVRDFGAIDDGKTLNTKAIQQAIDSC- 183
Query: 71 SFADKGGAKLFVPAGQWLTGSFDLISHLTLWLDKDAVILGSTNSDTWPV---IDPLPSYG 127
K G ++ +PAG + +G+ L S +TL L A++LGS N D +P + P +
Sbjct: 184 ----KPGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSENPDDYPAGYRLYPYSTIE 239
Query: 128 RGRELPGGRHRSLIFGRNLTDVVITGDNGTIDGQGSIWWEWFRNGTLDYT---------- 177
R L + ++ ITG +G IDG G W R T + T
Sbjct: 240 RPASLINAIDPNNSKPGTFRNIRITG-SGVIDGNG-----WLRAKTAEITDELGRSLPQY 293
Query: 178 ------------------------------------RPHLVELMNSTGVIISNLTFLNPP 201
R L+ L V ++ T NP
Sbjct: 294 VASKNSKVHEDGILAKNQVEKAVSDGMDLKNAYGQRRSSLMTLRGVENVYLAGFTVRNPA 353
Query: 202 FWTIHPVYCSHVKVQNVTIRAPLDSPNTDGIDPDSSDDVCIKDCYISTGDDLVSIKSGWD 261
F I + +H V N I D+ N DGI+ +S +V + + + TGDD ++ +G
Sbjct: 354 FHGIMNLE-NHNVVANGLIHQTYDANNGDGIEFGNSQNVMVFNNFFDTGDDCINFAAGTG 412
Query: 262 EYGISYGRPSTKITIHG---LIGETKLGAG-IAIGSEMSGGVSEVHAENLYFFNSVRGIR 317
E + + + G ++G G I GS + ++ AEN + + G+R
Sbjct: 413 E------KAQEQEPMKGAWLFNNYFRMGHGAIVTGSHTGAWIEDILAENNVMYLTDIGLR 466
Query: 318 IKTSPGRGGYVRNISISNVTLNHV--DVAIIFTGHFGEHPDDSYDPSALP------IIER 369
K++ GG RN++ N + + V ++ + + + Y P+ +P ++
Sbjct: 467 AKSTSTIGGGARNVTFRNNAMRDLAKQVMVMTLDYADSNANIDYPPAKIPAQFYDFTLKN 526
Query: 370 ITIKNVIGENVKMAGQLEGIEGDT-----FRYICLSNIKLNGVS 408
+T+ N G+N + I+GDT R + ++N++LN V+
Sbjct: 527 VTVDNSTGKNPSIE-----IKGDTANKAWHRLVHVNNVQLNNVT 565
>pdb|1BHE|A Chain A, Polygalacturonase From Erwinia Carotovora Ssp. Carotovora
Length = 376
Score = 93.2 bits (230), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 97/345 (28%), Positives = 153/345 (44%), Gaps = 36/345 (10%)
Query: 87 WLTGSFDLISHLTLWLDKDAVILGSTNSDTWPVIDPLPSYGRGRELPGGRHRSLIFGRNL 146
+L+G L S ++L +DK + N+ ++ + PS + G + I +
Sbjct: 52 FLSGPLSLPSGVSLLIDKGVTLRAVNNAKSF---ENAPSSCGVVDKNGKGCDAFITAVST 108
Query: 147 TDVVITGDNGTIDGQGSI--------WWEWFRNGT---LDYTRPHLVELMNSTGVIISNL 195
T+ I G GTIDGQG + WWE + L P L+++ S + N+
Sbjct: 109 TNSGIYGP-GTIDGQGGVKLQDKKVSWWELAADAKVKKLKQNTPRLIQINKSKNFTLYNV 167
Query: 196 TFLNPPFWTIHPVYCSH--VKVQNVTIRAPLDSPNTDGIDPDSSDDVCIKDCYISTGDDL 253
+ +N P + H V+ TI+ P + NTDGIDP SS ++ I I+TGDD
Sbjct: 168 SLINSPNF--HVVFSDGDGFTAWKTTIKTPSTARNTDGIDPMSSKNITIAYSNIATGDDN 225
Query: 254 VSIKSGWDEYGISYGRPSTKITIHGLIGETKLGAGIAIGSEMSGGVSEVHAENLYFFNSV 313
V+IK+ GR T+ I L + G G++IGSE + GV V ++L +
Sbjct: 226 VAIKA-------YKGRAETR-NISILHNDFGTGHGMSIGSE-TMGVYNVTVDDLKMNGTT 276
Query: 314 RGIRIKTSPGRGGYVRNISISNVTLNHVDVAIIFTGHFGEHPDDSYDPSALPIIERITIK 373
G+RIK+ G V + SNV + +V I+ + + + S +P IT K
Sbjct: 277 NGLRIKSDKSAAGVVNGVRYSNVVMKNVAKPIVIDTVY-----EKKEGSNVPDWSDITFK 331
Query: 374 NVIGENVKMAGQLEGIEGDTFRYICLSNIKLNGVSESPWNCSYIQ 418
+V E K L G + + N+KL S+S W +
Sbjct: 332 DVTSE-TKGVVVLNGENAKKPIEVTMKNVKL--TSDSTWQIKNVN 373
>pdb|1IA5|A Chain A, Polygalacturonase From Aspergillus Aculeatus
pdb|1IB4|A Chain A, Crystal Structure Of Polygalacturonase From Aspergillus
Aculeatus At Ph4.5
pdb|1IB4|B Chain B, Crystal Structure Of Polygalacturonase From Aspergillus
Aculeatus At Ph4.5
Length = 339
Score = 58.5 bits (140), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 69/246 (28%), Positives = 108/246 (43%), Gaps = 31/246 (12%)
Query: 147 TDVVITGDNG-TIDGQGSIWWEWFRNGTLDYTRPHLVELMNSTGVIISNLTFLNPPFWTI 205
+D+ ITG +G +I+G GS WW+ G T+P + T +IS L +N P
Sbjct: 72 SDLTITGASGHSINGDGSRWWDG-EGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVF 130
Query: 206 HPVYCSHVKVQNVTIRAPLDSPN----TDGIDPDSSDDVCIKDCYISTGDDLVSIKSGWD 261
++ ++++TI N TD D +S V I + DD V++ SG +
Sbjct: 131 SVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGEN 190
Query: 262 EYGISYGRPSTKITIHGLIGETKLGAGIAIGSEMSGGVSEVHAENLYF-----FNSVRGI 316
Y S G S G G++IGS GG S+ +N+ F NS G+
Sbjct: 191 IY-FSGGYCSG-------------GHGLSIGSV--GGRSDNTVKNVTFVDSTIINSDNGV 234
Query: 317 RIKTSPGRGGYVRNISISNVTLNHV-DVAIIFTGHFGEHPDDSYDPSALPIIERITIKNV 375
RIKT+ G V +++ ++TL + I+ ++G D S P+ I + NV
Sbjct: 235 RIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYG---DTSSTPTTGVPITDFVLDNV 291
Query: 376 IGENVK 381
G V
Sbjct: 292 HGSVVS 297
>pdb|1HG8|A Chain A, Endopolygalacturonase From The Phytopathogenic Fungus
Fusarium Moniliforme
Length = 349
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 65/227 (28%), Positives = 102/227 (44%), Gaps = 49/227 (21%)
Query: 140 LIFGRNLTDVVITGDNG-TIDGQGSIWWEWFRNGTLDYTRP-HLVELMNSTGVIISNLTF 197
+I G N+T ITG +G IDG G +W+ + + +P H + + +TG S +T
Sbjct: 65 VISGSNIT---ITGASGHVIDGNGQAYWDGKGSNSNSNQKPDHFIVVQKTTGN--SKITN 119
Query: 198 LNPPFWTIHPVYCSHVK-VQNVTIRAPL------DSPN-----------TDGIDPDSSDD 239
LN W PV+C + +TI + D PN TDG D SSD
Sbjct: 120 LNIQNW---PVHCFDITGSSQLTISGLILDNRAGDKPNAKSGSLPAAHNTDGFDISSSDH 176
Query: 240 VCIKDCYISTGDDLVSIKSGWDEYGISYGRPSTKITIHGLIGETKLGAGIAIGSEMSGGV 299
V + + ++ DD V++ SG T I + + G G++IGS GG
Sbjct: 177 VTLDNNHVYNQDDCVAVTSG------------TNIVVSNMY--CSGGHGLSIGSV--GGK 220
Query: 300 SEVHAENLYFF-----NSVRGIRIKTSPGRGGYVRNISISNVTLNHV 341
S+ + + F NS G RIK++ G G + N++ N+ L ++
Sbjct: 221 SDNVVDGVQFLSSQVVNSQNGCRIKSNSGATGTINNVTYQNIALTNI 267
>pdb|2IQ7|A Chain A, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|B Chain B, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|C Chain C, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|D Chain D, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|E Chain E, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|F Chain F, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
pdb|2IQ7|G Chain G, Crystal Structure Of The Polygalacturonase From
Colletotrichum Lupini And Its Implications For The
Interaction With Polygalacturonase- Inhibiting Proteins
Length = 339
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 62/203 (30%), Positives = 86/203 (42%), Gaps = 23/203 (11%)
Query: 147 TDVVITGDNG-TIDGQGSIWWEWFRNGTLDYTRPHLVELMNSTGVIISNLTFLNPPFWTI 205
T++ I G +G +ID QGS WW+ + T+P + I L LN P
Sbjct: 68 TNININGASGHSIDCQGSRWWD-SKGSNGGKTKPKFFYAHSLKSSNIKGLNVLNTPVQAF 126
Query: 206 HPVYCSHVKVQNVTI-RAPLDSP---NTDGIDPDSSDDVCIKDCYISTGDDLVSIKSGWD 261
+ + V +V I + DS NTD D SS V I + DD ++I SG
Sbjct: 127 SINSATTLGVYDVIIDNSAGDSAGGHNTDAFDVGSSTGVYISGANVKNQDDCLAINSG-- 184
Query: 262 EYGISYGRPSTKITIHGLIGETKLGAGIAIGS---EMSGGVSEVHAENLYFFNSVRGIRI 318
T IT G G G G++IGS V V N NS G+RI
Sbjct: 185 ----------TNITFTG--GTCSGGHGLSIGSVGGRSDNTVKTVTISNSKIVNSDNGVRI 232
Query: 319 KTSPGRGGYVRNISISNVTLNHV 341
KT G G V ++ S +TL+++
Sbjct: 233 KTVSGATGSVSGVTYSGITLSNI 255
>pdb|1NHC|A Chain A, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|B Chain B, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|C Chain C, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|D Chain D, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|E Chain E, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|F Chain F, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
Length = 336
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 72/260 (27%), Positives = 105/260 (40%), Gaps = 31/260 (11%)
Query: 143 GRNLTDVVITGDNGTIDGQGSIWWEWFRNGTLDYTRPHLVELMNSTGVIISNLTFLNPPF 202
G++LT V D IDG GS WW+ + T+P + + + + N P
Sbjct: 67 GKDLT--VTMADGAVIDGDGSRWWD-SKGTNGGKTKPKFMYIHDVEDSTFKGINIKNTPV 123
Query: 203 WTIHPVYCSHVKVQNVTIRAPLDSPN----TDGIDPDSSDDVCIKDCYISTGDDLVSIKS 258
I V ++V + + TI N TDG D S V I + DD ++I S
Sbjct: 124 QAI-SVQATNVHLNDFTIDNSDGDDNGGHNTDGFDISESTGVYISGATVKNQDDCIAINS 182
Query: 259 GWDEYGISYGRPSTKITIHGLIGETKLGAGIAIGSEMSGG-----VSEVHAENLYFFNSV 313
G I+ G G G G++IGS GG V V + NS
Sbjct: 183 G------------ESISFTG--GTCSGGHGLSIGS--VGGRDDNTVKNVTISDSTVSNSA 226
Query: 314 RGIRIKTSPGRGGYVRNISISNVTLNHV-DVAIIFTGHFGEHPDDSYDPSALPIIERITI 372
G+RIKT G V I+ SN+ L+ + D I+ + E+ + PS I +T+
Sbjct: 227 NGVRIKTIYKETGDVSEITYSNIQLSGITDYGIVIEQDY-ENGSPTGTPSTGIPITDVTV 285
Query: 373 KNVIGENVKMAGQLEGIEGD 392
V G A Q+ + GD
Sbjct: 286 DGVTGTLEDDATQVYILCGD 305
>pdb|1CZF|A Chain A, Endo-Polygalacturonase Ii From Aspergillus Niger
pdb|1CZF|B Chain B, Endo-Polygalacturonase Ii From Aspergillus Niger
Length = 362
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 61/239 (25%), Positives = 99/239 (41%), Gaps = 29/239 (12%)
Query: 149 VVITGDNG-TIDGQGSIWWEWFRNGTLDYTRPHLVELMNSTGVIISNLTFLNPPFWTIHP 207
+ +TG +G I+ G+ WW+ GT +P I+ L N P
Sbjct: 97 ITVTGASGHLINCDGARWWD--GKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAF-S 153
Query: 208 VYCSHVKVQNVTIR-APLDSP---NTDGIDPDSSDDVCIKDCYISTGDDLVSIKSG---W 260
V + + +VTI A D+ NTD D +S V I ++ DD +++ SG W
Sbjct: 154 VQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIW 213
Query: 261 DEYGISYGRPSTKITIHGL-IGETKLGAGIAIGSEMSGGVSEVHAENLYFFNSVRGIRIK 319
G G HGL IG ++G + V V E+ NS +RIK
Sbjct: 214 FTGGTCIGG-------HGLSIG--------SVGDRSNNVVKNVTIEHSTVSNSENAVRIK 258
Query: 320 TSPGRGGYVRNISISNVTLNHV-DVAIIFTGHFGEHPDDSYDPSALPIIERITIKNVIG 377
T G G V I+ SN+ ++ + D ++ + E + P+ I+ + +++V G
Sbjct: 259 TISGATGSVSEITYSNIVMSGISDYGVVIQQDY-EDGKPTGKPTNGVTIQDVKLESVTG 316
>pdb|2VBK|A Chain A, Native Tailspike Protein Of Bacteriophage Sf6
pdb|2VBM|A Chain A, Tailspike Protein Of Bacteriophage Sf6 Complexed With
Tetrasaccharide
Length = 514
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 41 HSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTG 90
++SI +FG + DGVT N +A QNAI + S G +LF+PA G
Sbjct: 50 EAISILDFGVIDDGVTDNYQAIQNAIDAVASLPS--GGELFIPASNQAVG 97
>pdb|2VBE|A Chain A, Tailspike Protein Of Bacteriophage Sf6
Length = 514
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 41 HSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTG 90
++SI +FG + DGVT N +A QNAI + S G +LF+PA G
Sbjct: 50 EAISILDFGVIDDGVTDNYQAIQNAIDAVASLPS--GGELFIPASNQAVG 97
>pdb|3SUC|A Chain A, Crystal Structure Of The Pre-Mature Bacteriophage Phi29
Gene Product 12
Length = 772
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 25/113 (22%)
Query: 35 LEVFRPHSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTGSFDL 94
++ + VS+ +GA GDGVT + +AF+ AI + G ++VP G ++
Sbjct: 15 IDELKQFGVSVKTYGAKGDGVTDDIRAFEKAI--------ESGFPVYVPYGTFMVSR--- 63
Query: 95 ISHLTLWLDKDAVILGSTNSDTWPVIDPLPSYGRGRELPGGRHRSLIFGRNLT 147
+ L + V+ G+ + VI + S GRG SL++ N+T
Sbjct: 64 ----GIKLPSNTVLTGAGKRN--AVIRFMDSVGRG--------ESLMYNENVT 102
>pdb|3GQ7|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment
pdb|3GQ8|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In Complex With
2-(N-Cyclohexylamino)ethane Sulfonic Acid (Ches)
pdb|3GQ9|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In An Apo Form
pdb|3GQA|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In Complex With Cobalt Ions
Length = 609
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 46/98 (46%), Gaps = 17/98 (17%)
Query: 35 LEVFRPHSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTGSFDL 94
++ + VS+ +GA GDGVT + +AF+ AI + G ++VP G ++
Sbjct: 15 IDELKQFGVSVKTYGAKGDGVTDDIRAFEKAI--------ESGFPVYVPYGTFMV----- 61
Query: 95 ISHLTLWLDKDAVILGSTNSDTWPVIDPLPSYGRGREL 132
+ L + V+ G+ + VI + S GRG L
Sbjct: 62 --SRGIKLPSNTVLTGAGKRN--AVIRFMDSVGRGESL 95
>pdb|1K5C|A Chain A, Endopolygalacturonase I From Stereum Purpureum At 0.96 A
Resolution
pdb|1KCC|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With A Galacturonate At 1.00 A Resolution.
pdb|1KCD|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With Two Galacturonate At 1.15 A Resolution
Length = 335
Score = 35.0 bits (79), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 91/218 (41%), Gaps = 41/218 (18%)
Query: 159 DGQGSIWWEW--FRNGTLDYTRPHLVELMNSTGVIISNLTFLNPPFWTIH--PVYCSHVK 214
DG G+++W+ NGT +PH + +G LN P I P +H+
Sbjct: 78 DGNGALYWDGKGTNNGTH---KPHPFLKIKGSGTY-KKFEVLNSPAQAISVGPTD-AHLT 132
Query: 215 VQNVTIRAPLDSP-----NTDGIDPDSSDDVCIKDCYISTGDDLVSIKSGWDEYGISYGR 269
+ +T+ NTDG D S+++V I++C + DD ++I G +
Sbjct: 133 LDGITVDDFAGDTKNLGHNTDGFDV-SANNVTIQNCIVKNQDDCIAINDGNN-------- 183
Query: 270 PSTKITIHGLIGETKLGAGIAIGSEMSGG-VSEVHAENLYFFNSVRGIRIKTSPGRGGYV 328
I + G GI+IGS +G VS V + S+ G+RIK
Sbjct: 184 ------IRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQR----TA 233
Query: 329 RNISISNVTLNHVDVAIIFTGHFG-----EHPDDSYDP 361
+ S+S VT + ++ I +G +PDD +P
Sbjct: 234 TSASVSGVTYDANTISGI--AKYGVLISQSYPDDVGNP 269
>pdb|4A25|A Chain A, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|B Chain B, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|C Chain C, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|D Chain D, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions
Length = 169
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 39 RPHSVSITEFGAVGDGVTLNTKAFQNAIFYLNSFADKGGAKLFVPAGQWLTGSFDLISHL 98
RP +V+ + G VG ++T+A AI L ++ P S DL+ +
Sbjct: 90 RPQTVAASRIGDVGPD-EIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAI 148
Query: 99 TLWLDKDAVILGSTN 113
TL L+K A ++GS N
Sbjct: 149 TLELEKQAWMIGSEN 163
>pdb|1BFO|A Chain A, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|C Chain C, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|E Chain E, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|G Chain G, Campath-1g Igg2b Rat Monoclonal Fab
Length = 214
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 18/29 (62%)
Query: 49 GAVGDGVTLNTKAFQNAIFYLNSFADKGG 77
+VGD VTLN KA QN YLN + K G
Sbjct: 13 ASVGDRVTLNCKASQNIDKYLNWYQQKLG 41
>pdb|4FDW|A Chain A, Crystal Structure Of A Leucine Rich Hypothetical Protein
(Bacova_01565) From Bacteroides Ovatus Atcc 8483 At 2.05
A Resolution
Length = 401
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 382 MAGQLEGIEGDTFRYICLSNIKLNGVSESPWNCSYIQG-YSDLVFPETCDPLKESIFPMH 440
+ ++ I D FR ++ + LN +S + ++ ++VFP T + LKE IF
Sbjct: 120 LPNSVKSIPKDAFRNSQIAKVVLNEGLKSIGDXAFFNSTVQEIVFPSTLEQLKEDIF--- 176
Query: 441 HLDCYDLSNHFRSSRNQKRLARL 463
CY+L ++ ++ ++ +L
Sbjct: 177 -YYCYNLK---KADLSKTKITKL 195
>pdb|3QPX|L Chain L, Crystal Structure Of Fab C2507
Length = 213
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 49 GAVGDGVTLNTKAFQNAIFYLNSFADKGG 77
+VGD VTL+ KA QN YLN + K G
Sbjct: 13 ASVGDRVTLSCKASQNIYNYLNWYQQKLG 41
>pdb|2ABI|A Chain A, Crystal Structure Of The Human Mineralocorticoid Receptor
Ligand-Binding Domain Bound To Deoxycorticosterone
pdb|2ABI|B Chain B, Crystal Structure Of The Human Mineralocorticoid Receptor
Ligand-Binding Domain Bound To Deoxycorticosterone
pdb|2ABI|C Chain C, Crystal Structure Of The Human Mineralocorticoid Receptor
Ligand-Binding Domain Bound To Deoxycorticosterone
Length = 256
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 51/121 (42%), Gaps = 21/121 (17%)
Query: 336 VTLNHVDVAIIFTGHFGEHPDDSYDPSALPIIERITIKNVIGENVKMAGQLEGIEG---- 391
+ L +++ I++ G+ PD + + L + R+ K +I + VK A L G +
Sbjct: 12 MVLENIEPEIVYAGYDSSKPDTA--ENLLSTLNRLAGKQMI-QVVKWAKVLPGFKNLPLE 68
Query: 392 -----DTFRYICLSNIKLNGVSESPWNCSYIQGYSDLVFPETCDPLKESIFPMHHLDCYD 446
+ ++CLS+ L+ S N ++ DLVF E MH Y+
Sbjct: 69 DQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEE---------KMHQSAMYE 119
Query: 447 L 447
L
Sbjct: 120 L 120
>pdb|3H09|A Chain A, The Structure Of Haemophilus Influenzae Iga1 Protease
pdb|3H09|B Chain B, The Structure Of Haemophilus Influenzae Iga1 Protease
Length = 989
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 14 LALFSEAPWAVAGSSQCSQSNLEVFRPHSVSITEFGAVG--DGVTLNTKAFQNAIFYLNS 71
+ L + W + G S +Q NL+ H + + V + +T+N+ + + +YL
Sbjct: 827 VRLTENSHWHLTGDSNVNQLNLDKGHIHLNAQNDANKVTTYNTLTVNSLSGNGSFYYLTD 886
Query: 72 FADKGGAKLFVPAGQWLTGSFDL 94
++K G K+ V + TG+F L
Sbjct: 887 LSNKQGDKVVVT--KSATGNFTL 907
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.138 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,439,439
Number of Sequences: 62578
Number of extensions: 729348
Number of successful extensions: 1621
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1588
Number of HSP's gapped (non-prelim): 32
length of query: 466
length of database: 14,973,337
effective HSP length: 102
effective length of query: 364
effective length of database: 8,590,381
effective search space: 3126898684
effective search space used: 3126898684
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)